- Heroes: Raiden, Liu Kang, Sonya, Johnny Cage, Kung Lao, Jax, Kitana, Jade, Stryker, Kuai Liang, Smoke, Nightwolf, Kenshi, and Scorpion.
- Villains: Shao Kahn, Mileena, Quan Chi, Bi Han, Skarlet, Rain, Shang Tsung, Scorpion, Kintaro, Goro, Kano, Sheeva, Noob Saibot, Baraka, Sektor, Reptile, Kia, Jataaka, Sareena, Tanya, and Motaro.
- Evil to Good: Cyrax, Sindel, Kabal, and Ermac.
PART 1:
- It would still be about Raiden going back in the past, making this game a reboot.
- Shang Tsung and Quan Chi kill Scorpion's Clan. They were able to do it by having Shang Tsung morph into Bi Han, making Scorpion think that Bi Han was responsible for the deaths of his clan members.
- Kenshi gets blinded by Shang Tsung and is left to die. Luckily, Raiden finds him and heals him even though he remains blind.
- Stryker, Sonya, and Jax work together as law enforcement officers.
- Kabal is in the Black Dragon with Kano during the first tournament.
- Cyrax and Sektor fight each other as humans because Cyrax wants to quit the Lin Kuei. However, the Lim Kuei Cyborgs managed to ambush the two and turn them into cyborgs as well.
- Scorpion kills Bi Han.
- Liu Kang defeats Shang Tsung in the first tournament. Kahn turns the sorcerer young and gives him another chance.
PART 2:
- Kitana finds out that Mileena is in the Flesh Pit. The two fight but is stopped by Shang Tsung. Kitana gets pissed at the sorcerer for making a clone of her and finding out that the emperor knew all about this the whole time so she secretly betrays them by joining the heroes.
- Jade attempts to stop Kitana for her betrayal but found out that she can no longer be a slave, so she decided to join the princess.
- Tanya and Rain find out that Kitana and Jade betrayed them so they fight. Jade jams her pole onto Rain's groin while Kitana kicks Tanya hard at the nose. So Kitana and Jade emerge victorious.
- Jax and Johnny Cage fight over Sonya but she makes them stop.
- Ermac emerges and rips out Jax's arms with his telekenesis. Then, Ermac fights Sonya and Johnny Cage and still defeats the two with his powers. After that, Ermac is blown to the wall with an unknown force of energy. That energy is Kenshi's. He tells Sonya and Cage to help Jax while he fights off against Ermac. Kenshi emerges victorious but Ermac flees.
- Jax gets his new pair of arms.
- Kitana and Jade join the heroes.
- Kitana and Liu Kang fight Mileena and Baraka. Liu Kang kills Baraka with an uppercut decapitation while Mileena flees away before Kitana can finish her off.
- Raiden fights Sheeva and defeats her.
- Johnny fights Reptile and gets defeated.
- Smoke is turned into a cyborg by the Lin Kuei.
- Kabal betrays Kano and decides to join the forces of good. He also becomes Stryker's best friend.
- Kabal and Stryker fight Goro and Kintaro. During the fight, Kintaro attempts to blow flames at Stryker but Kabal took the burn for him. Then, Raiden and Nightwolf attack the two Shokans with lightning bolts, making the monsters flee the scene. Stryker desperately begs Raiden to keep Kabal alive. They were able to keep him alive but they couldn't heal his burnt skin. So he had to be on oxygen the whole time with a mask.
- Sonya fights Skarlet and kicks her into the Acid Pool.
- Kuai Liang fights Scorpion. Scorpion escapes afterwards.
- Kuai Liang is ambushed by Sektor, Cyrax, and Smoke with other cyborgs, trying to turn him into a cyborg as well but is rescued Nightwolf, Kenshi, and Raiden.
- Kung Lao and Liu Kang fight Quan Chi and Shang Tsung in the second tournament. Shaolin monks win and because Shang Tsung blew his second chance, Kahn kills the emperor but spares Quan Chi, who is severely beaten still.
- Kung Lao and Liu Kang fight Goro and Kintaro. Kung Lao splits Kintaro vertically in half with his hat while Liu Kang turns into a dragon and bites off Goro's upper torso.
- Kung Lao tries to fight Kahn but ends up cripples with Kahn's hammer smashing his leg. So Liu Kang fights the emperor and punches a hole through his chest.
- Liu Kang becomes the champion of the second tournament.
Part 3:
- Shao Kahn is recovered by Quan Chi.
- Quan Chi resurrects Bi Han (as Noob Saibot) and Sindel.
- Earthrealm gets taken over. Mileena, Quan Chi, Tanya, Sheeva, Kia, Jataaka, Sareena, Smoke, Sektor, and Rain, Cyrax are invading the streets. Quan Chi watches them fight.
- Jade vs Tanya. Tanya flees afterwards.
- Kitana vs Mileena. Mileena gets knocked out.
- Sonya vs Kano. Sonya manages to toss him down the subway tracks, making him get run over by a train.
- Nightwolf vs Sheeva. Nightwolf stabs his knives on Sheeva's shoulders and does the Ascention fatality on her.
- Kuai Liang vs Smoke. Kuai Liang defeats him and makes him regain his memories again. Then Smoke joins the heroes.
- Kabal vs Jataaka. Kabal decapitates her with his hooksword.
- Stryker vs Kia. Stryker shoots her at the head.
- Kenshi vs Sareena. Sareena flees afterwards.
- Kung Lao vs Rain. Rain gets knocked out.
- Liu Kang vs Motaro. Liu Kang has difficulty facing off against the centaur.
- Raiden vs Cyrax. Raiden slowly convinces Cyrax to join the heroes, which was successful.
- Raiden helps Liu Kang defeat Motaro but don't know he is still alive.
- Many innocents have been captured by Quan Chi, Shao Kahn and their minions to take their souls. The heroes will attempt to rescue them.
- Kitana and Jade find Sindel and Ermac try to convince her to turn good again.
- Kitana and Jade vs Sindel and Ermac. Jade and Kitana have difficulty convincing the queen to regain her true identity as a loving mother so she beats up the two. With Kitana moaning in pain, Ermac resists to attack. A Jerrod's soul takes over Ermac's body. Then he uses his powers to stop Sindel. He talks to her and begs her to remember all the good times as the queen of Edenia and as a mother of Kitana. Sindel begins to see Jerrod and tears drop down her face and hugs him. The family that was once lost, has been restored again.
- Unfortunately, the family reunion was short lived when sais strike at the queen's chest and a lightning bolt strikes Ermac (Jerrod).
- Mileena and Rain interrupt the family bonding and attack.
- Mileena vs Kitana. Kitana decapitates her with anger.
- Jade vs Rain. Jade vertically impales him with her pole weapon and makes the weapon retract into a small stick again, keeping it for herself.
- Sindel says goodbye to Kitana, Jade, and Jerrod (who all cry)
- Tanya sneaks behind Jerrod and impales him at the back with her Kobu Jutsi blades.
- Kitana and Jade vs Tanya. Unfortunately, Tanya still manages to flee.
- Jade and Kitana say there goodbyes to Jerrod too and rescue the group of ppl that are there with them.
- In place, Kuai Liang, Smoke, and Cyrax find Sektor and the Lin Kuei with innocent ppl held captive.
- Kuai Liang, Smoke, and Cyrax vs Sektor and Lin Kuei Cyborgs. Cyrax decapitates Sektor with his buzzsaw.
- Kuai Liang, Smoke, and Cyrax rescue the innocent.
- Not far away, Noob Saibot and Quan Chi have innocents held captive. Kuai Liang leaves Cyrax and Smoke so he can rescue the other batch of innocents. Unfortunately, Quan Chi has already killed the ppl with his sorcery, forming a soulnado.
- Kuai Liang vs Noob Saibot and Quan Chi. Kuai Liang has difficulty fighting the two. But then NIGHTWOLF joins him. Kuai Liang is able to deep freeze Noob and shatter him but Quan Chi escapes.
- The heroes group up, preparing for a final battle. But then, they are ambushed by Motaro (who is weilding a lance) and 50 Tarkatans.
- Raiden, Jax, Liu Kang, Sonya, Johnny Cage, Kitana, Jade, Kabal, Stryker, Cyrax, Smoke, Kung Lao, and Kuai Liang vs Motaro and 50 Tarkatans. The Tarkatans were beaten but Motaro kills Smoke, Cyrax, Stryker, Kabal, Jax, and Sonya while badly injuring the rest. After finding out that Sonya died, Johnny has tears running down his face. He begins to lose control of his powers so he kills Motaro. Then he falls exhausted.
- Kahn appears while Raiden gets up.
- Raiden vs Kahn. Kahn defeats Raiden.
- Liu Kang, Kung Lao, Kitana, and Jade vs Shao Kahn. After a long battle, the four defeat the emperor with Liu Kang doing the finishing move.
ENDING:
- The remaining heroes plan to restore Earthrealm.
- Quan Chi, Tanya, and Sareena have a conference with Shinnok plotting their next move to take over all realms.